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2020

Congrats to VGL undergrad Steven Palomares on his acceptance into the NSF LSAMP/California Alliance for Minority Participation (CAMP) Program for the 2020-2021 academic year.

The NSF LSAMP/CAMP program is a UC Davis undergraduate research program designed to increase the number of underrepresented students who pursue research in Science, Technology, Engineering, and Mathematics (STEM) fields by offering students the chance to work on faculty-sponsored research projects relevant to their interests. CAMP offers extensive resources, organized workshops, and unique opportunities for participants to excel in their respective fields of study.

Welcome to our newest member, Will Sharpee. Will is our new Scientific Program Manager.

JOB OPENING

Open until filled

Postdoctoral Research Fellow Position
Population Genomics

Description:
The Vector Genetics Lab (VGL) at the University of California, Davis has a post-doctoral position available for a highly motivated candidate with a background in population genetics/genomics. The VGL is dedicated to research and training in the areas of population & molecular genetics, genomics and bioinformatics of insect vectors of human and animal disease. We have developed a program aimed at expanding knowledge that may be applied to improving control of disease vectors and that also addresses problems of interest in the field of evolutionary genetics. See details at: https://vectorgeneticslab.ucdavis.edu/

Ongoing projects include work on the following systems:
– Populations of Anopheles malaria mosquitoes on islands off the coast of Africa
– Invasive Aedes aegypti populations in California

Ongoing research topics include:
– Interspecific hybridization and introgression as a mechanism for adaptation
– The evolution of populations on isolated islands
– Development of new whole genome-based methods to estimate population size and dispersal
– Evaluating the behavior of Cas9-based gene drive systems via field trials

Responsibilities:
The successful candidate will work on whole-genome sequencing data sets to decipher recent population history and evolution in mosquitoes that are vectors of human diseases.

Required Qualifications:
– PhD in Population Genetics/Genomics, Bioinformatics, or related discipline (theoretical and/or applied)
– In-depth knowledge of population genetics theory
– Demonstrated record of research productivity and publications

Preferred Qualifications:
– Experience working in Linux environment
– Experience with genomic data analysis
– Experience with coalescence/IBD methods
– Programming experience (e.g. C/C++, Python/Perl, R)
– Strong mathematical/statistical skills

Salary:
This is a full-time position. Salary is commensurate with qualifications and experience.

How to apply:
Applicants should submit the following materials:
– A cover letter
– A curriculum vitae
– List of relevant publications
– Contact information for 3 referees
Send the above combined into a single PDF to Gregory Lanzaro at vectorgeneticslab@gmail.com
Review of applications will start immediately. This position will be open until filled. The appointment is for a duration of two years.

The University of California is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age or protected veteran status. For the complete University of California nondiscrimination and affirmative action policy see:
http://policy.ucop.edu/doc/4000376/NondiscrimAffirmAct.

August

Science Visitor and Colloquium Program – Earth Science Seminar

Adaptation of Aedes aegypti in California: Understanding the Genomic Basis of Adaptation and Predicting Adaptive Genetic Variation under Projected Future Climates Based on Multivariate Models
Presented by Shaghayegh Soudi
Post-doctoral research fellow at the Department of Pathology, Microbiology and Immunology, University of California, Davis

Thursday, August 20, 2020
Virtual Event starts at 3:00 P.M.

Abstract
Population differentiation (PD) and ecological association (EA) tests have recently emerged as prominent statistical methods to investigate signatures of local adaptation using population genomic data. Spatially varying selection triggers differential adaptation of local populations. Here, we mined the determinants of local adaptation at the genome-wide scale in an invasive species “Aedes aegypti”. A. aegypti is the yellow fever mosquito, a mosquito that can spread dengue fever, chikungunya, Zika fever, Mayaro and yellow fever viruses, and other disease agents. In the summer of 2013, A. aegypti Linnaeus was first detected in three cities in central California (Clovis, Madera and Menlo Park). It has now been detected in multiple locations in central and southern California as far south as San Diego and Imperial Counties. A number of published reports suggest that California populations have been established from multiple independent introductions. We analyzed 1,272,134 SNPs identified from whole genome sequencing data from twelve populations of A. aegypti distributed in California to identify evidence of adaptation using three different genome scan methods. We have found some genes relevant to thermal tolerance such as heat shock proteins by all three methods. In addition, the outbreak risk of invasive species caused by rapid climatic shifts requires accurate models for predicting species’ responses. Despite evidence that evolutionary adaptation could mitigate climate change impacts, evolution is rarely integrated into predictive models. Integrating population genomics and environmental data, we are now trying to identify genomic variation associated with climate across the distribution range of A. aegypti in California.

About the Speaker
Dr. Soudi received a Ph.D. in evolutionary biology from Bielefeld University, in Bielefeld, Germany. After a two-year post-doctoral scholarship in bio-computational molecular evolution at the Biological Sciences department of the University of Calgary in Alberta, Canada, Dr. Soudi joined Prof. Greg Lanzaro’s lab at U.C. Davis, where she is working on a landscape genetics project examining populations of Aedes aegypti in California, as well as the UCI Malaria Initiative.

 
JPL Contacts: If you would like to meet (remotely) with the speaker, please contact Ziad Haddad (4-1218).

WebEx:  https://jpl.webex.com/jpl/j.php?MTID=m0daae0f4bf83294191e442890bf78c3b

                 Meeting number (access code): 199 187 7518
                 Meeting password: baodai

JOB OPENING

–FILLED–

ACAD PRG MGT OFCR 3 (Scientific Program Manager)

Job Summary:

Under general direction of the Principal Investigator, develop, implement and provide ongoing scientific expertise, direction and management of multiple, large and complex, international scientific research programs impacting the overall success of a multi-campus, interdepartmental, global health malaria research project in selected field sites in Africa (specifically the Union of the Comoros and the Republic of Sao Tome and Principe). Assist and support the PI in planning and coordinating the scientific research aspects of the program and will work directly with individual post-doctoral researchers in ensuring the timely completion of individual components of the research agenda. Identify program objectives and strategies, manage very significant human, financial, and physical resources, and will function with a high degree of autonomy. Manage program timelines and deliverables, develop written reports, scientific papers, and presentations, and represent the program for diverse audiences. Collaborate, and work in partnership with, the Engagement Program Manager and Field Station Manager(s) at the African field sites.

Position Information:

Salary Range – $5,683.33-$11,408.33/Month
No. of Positions – 1
Appointment Type – Career
Percentage of Time – 100%
Shift Hours – Monday-Friday, 8am-5pm
Location – Davis
Union Representation – No
Benefits Eligible – Yes
Apply By Date – 6/28/2020

Essential Responsibilities:

SUPERVISORY DUTIES (60%)
-Provide scientific expertise needed to direct research projects and lab personnel.
-Work in regular collaboration and communication with Engagement Program Manager to ensure that entomology and engagement field teams are working together to achieve project goals and are adhering to project timeline.
-Hire, train and supervise staff; conduct performance appraisals; document and implement corrective actions and discipline; resolve disputes and complaints;
-Assign, supervise and monitor staff responsible for operating and maintaining the laboratory and insectary.
-Assist in the hiring and training of lab personnel.

PROJECT MANAGEMENT (30%)
-Assist in the preparation of manuscripts for publication in peer-reviewed scientific journals.
-Develop, review, and deliver presentations for diverse audiences including international stakeholders, undergraduate/graduate students, scientific researchers, international students, international communities, and public interest groups.
-Regularly communicate with scientific collaborators (national and international).
-Actively seek new funding sources to support scientific research and participate in the development of funding proposals and applications.
-Prepare regular project reports for project team and keep entire team informed about new and ongoing research programs and activities.
-Participate in the quarterly/annual review of program timeline, budget, and strategy.
-Assist in the development and review of scientific educational programs, materials, and tools for the engagement program (e.g. videos, educational booklets, and brochures) to ensure accuracy of scientific information.
-Represents the project in national and international meetings, conferences, workshops and discussions.
-Travel to field sites in Africa.

LABORATORY ADMINISTRATION (10%)
-Responsible for day to day management and operations of scientific research at the Vector Genetics Laboratory (VGL) at UCD.
-Collect, analyze and create scientific program reports and papers related to entomological field work in Africa.
-In collaboration with PI, develop written responses to published scientific work, prepare manuscripts, review manuscripts, and analyze and develop visual presentations of data.
-Analyze and review current laboratory protocols and procedures and suggest/develop improvement strategies.

Physical Demands:

-Remain in a stationary position, often standing or sitting for prolonged periods at a computer terminal.
-Occasionally works in outdoor weather conditions.
-This position requires travel to Africa on multiple 12+ hour long flights in economy level seating.
-Willing and able to travel regularly (domestic and international) with an understanding that there will be regular travel to field sites in Africa for up to 4-6 weeks at a time, multiple times during the year.

Work Environment:

-Moderate noise level in work environment.
-Work flexible schedule including occasional holidays and weekends on short notice to meet operational needs.
-Work in areas where hazardous materials are present.
-UC Davis is a smoke and tobacco free campus effective January 1, 2014. Smoking, the use of smokeless tobacco products, and the use of unregulated nicotine products (e-cigarettes) will be strictly prohibited on any UC Davis owned or leased property, indoors and outdoors, including parking lots and residential space.

Qualifications:

Required:
-Advanced degree in population genomics or a related field; or an equivalent combination of education and experience with minimum 5 years of postdoctoral research experience.
-Understanding of genetic engineering and gene drive research and proposed use of this technology for the eradication of vector-borne diseases.
-Skills and competency in genome assembly and annotation, sequence quality processing and analysis, e.g. Illumina, PacBio, Sanger, Oxford Nanopore and working in a Linux high performance computing environment.
-Expertise in programming languages (C++, Python, C, Java, Perl).
-Basic wet lab skills including DNA isolation, quantitation, and quality assessment, and NGS library prep.
-Exceptional communication skills: specifically experience communicating with diverse groups of people, in multiple languages and countries about complex scientific issues. Exceptional critical thinking and strategic planning skills; solution oriented. Exceptional writing skills.
-Experience leading teams, motivating others to remain goal oriented, focused and collaborative

Preferred:
-Advanced understanding of vector-borne diseases.
-Advanced understanding of genetic engineering, gene drive research and applications of the technology.
-Experience conducting field research in Africa.
-Advanced language skills in French or Portuguese.

Special Requirements:

Background Check

This position is a critical position and subject to a background check. Employment is contingent upon successful completion of background investigation including criminal history and identity checks.

EEO/AA Statement

The University of California is an Equal Opportunity/Affirmative Action Employer advancing inclusive excellence. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, protected veteran status, or other protected categories covered by the UC nondiscrimination policy.

April
Dr. Lanzaro has posted a blog post for Hanno’s Nature Communications paper here https://go.nature.com/3dZOoIB

March
Hanno’s paper Abundance of conserved CRISPR-Cas9 target sites within the highly polymorphic genomes of Anopheles and Aedes mosquitoeshas been published in Nature Communications. Congrats Hanno!

March
The city of Davis has issued a shelter in place request due to the COVID-19 virus. Up to date information can be found on  the UC Davis coronavirus information page and the VetMed Coronavirus Resources page

Due to the COVID-19 virus and the resulting travel restrictions, the Vector Genetics lab has canceled the planned travel to São Tomé and Príncipe and greatly curtailed work in the Comoros. Planning these trips takes a large amount of effort from most of our team and, while we are disappointed by the delay, we are hopeful that all our teams and partners both in the US and abroad remain healthy and that we will be able to re-schedule all travel soon.

March Greg is a confirmed speaker at the upcoming World Malaria Day Symposium on Malaria Vector Biology and Control at the Johns Hopkins Bloomberg School of Public Health in Baltimore, Maryland on Friday, 24 April 2020. Registration for this event is free.

February A few members of the VGL team are traveling to the Comoros islands for a month to collect mosquitoes for the UCIMI project.

February Dr. Yoosook Lee is representing the VGL at the PacVec annual meeting hosted by UC Riverside

January Several VGL team members are attending the UCIMI annual meeting in Irvine, CA. Greg Lanzaro will present about our team’s work over the past year.

2019

The VGL team traveled to São Tomé and Príncipe in December. While there we signed a partnership agreement with the local government and started collecting mosquitoes for the UCIMI project. We are very excited to continue our work there in 2020!

We are sad to say goodbye to insectary manager Kendra Person, postdoc Hanno Schmidt, and lab manager Allison Weakley. We wish them the best of luck for their futures!

Welcome aboard to our new hires! Postdocs: Melina Campos and Shaghayegh Soudi and community engagement staff: Ana Kormos and Joyce Imafidon.

Good luck to all our departing undergraduates, Parker Houston, Seerat Randhawa, and Mirsha Torres! We wish you the best of luck in your careers and education.

We are sad to say goodbye to postdoc Oscar Kirstein. We wish him the best of luck at his new position at Emory University!

Anopheles introgression in Burkina Faso paper published online. Congrats to all VGL members and alumni involved.

We are happy to welcome Travis Collier and Marc Crepeau to the VGL team!

2018

Parker Houston has been awarded an Undergraduate Travel Award for his travel to the ABRCMS Conference in November where he presented his poster “Design of a Multiplex SNP Assay for the Detection of Four Different Arboviruses Transmitted by Aedes Mosquitoes”

JOB OPENING

–FILLED–

Bioinformatics Programmer at the University of California, Davis

Job Summary:

Under general direction of the PI, responsible for program installation, writing data conversion scripts and pipelines for processing genome sequence data. Oversee large scale analysis of high throughput sequencing data. Maintain managed sites and data backup servers. Responsible for customization of existing tools for population genomics data analysis. Resolve web production issues and implement web architecture updates. Responsible for website management and support. 

Responsibilities:

The successful candidate will work on whole-genome sequencing data sets to decipher recent population history and evolution in mosquitoes that are vectors of human diseases. Further major responsibilities include extending and customizing state of the art methodologies in this field to implement bioinformatical pipelines tailored towards the specific needs of the various projects.

Minimum Qualifications:

– Graduate degree in biological science, bioinformatics, molecular sciences, or related area and/or equivalent experience/training.
– Experience with database administration on linux server, My SQL database, and/or web hosting.
– Familiarity with mosquito biology and molecular genetics.
– Experience in web-database interface such as python CGI, PHP, and Java
– Experience in data backup solutions and skill to maintain network attached storage device.
– Experience in any population genomic database and/or genome sequencing data analysis.
– Understanding of molecular genetics and laboratory procedures applicable to DNA sequencing analysis.
– Experience in technical writing of research publications.
– Interpersonal and oral communication skills to interact convey technical issues/solutions and to work with biologists and geography experts. 

Preferred Qualifications:

– Ph.D. degree in biological science, bioinformatics, molecular sciences, or related area and/or equivalent experience/training.
– Demonstrated knowledge of the biology and genomics of the mosquito vector, Anopheles gambiae.
– Skills on googlemap API and basic GIS.
– Project management skills to establish and carry out priorities and adapt to fluctuating workload.
– Experience in population genomics or population genetics data analysis.

Appointment Description:

100% Monday through Friday, 8am to 5pm, Contract dates 2/01/2019 – 2/01/2021

The University of California is an Equal Opportunity/Affirmative Action Employer advancing inclusive excellence. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, protected veteran status, or other protected categories covered by the UC nondiscrimination policy.

The VGL has received permission from the government in São Tomé and Príncipe to begin initial mosquito collections for the UCIMI project. Greg and several other team members will be making multiple trips to São Tomé and Príncipe in 2019. Photos to come!

JOB OPENING

–FILLED–

Postdoctoral Research Fellow Position in Population Genomics at the University of California, Davis

Description:

The Vector Genetics Lab (VGL) at the University of California, Davis has a post-doctoral position available for a highly motivated candidate with a background in population genomics. The VGL is dedicated to research and training in the areas of population & molecular genetics, genomics and bioinformatics of insect vectors of human and animal disease. We have developed a program aimed at expanding knowledge that may be applied to improving control of disease vectors and that also addresses problems of interest in the field of evolutionary genetics. See details at: https://vectorgeneticslab.ucdavis.edu/

Ongoing projects include work on the following systems:

  • Invasive Aedes aegypti populations in California
  • Island populations of Anopheles mosquitoes in islands off the coast of Africa.
  • Urban and island populations of Anopheles mosquitoes in India

Ongoing research topics include:

  • Interspecific hybridization and introgression as a mechanism for adaptation
  • The evolution of populations on isolated islands
  • Defining populations in urban centers as ecological islands
  • Development of new wgs-based methods to estimate population size and dispersal
  • Evaluating the behavior of gene drive systems via field trials

Responsibilities:

The successful candidate will work on whole-genome sequencing data sets to decipher recent population history and evolution in mosquitoes that are vectors of human diseases. Further major responsibilities include extending and customizing state of the art methodologies in this field to implement bioinformatical pipelines tailored towards the specific needs of the various projects.

Required Qualifications:

– PhD in Bioinformatics, Computational Biology, Population Genomics or related discipline (theoretical and/or applied)

– Strong background in statistics

– In-depth knowledge of population genetics theory

– Experience working in Linux environment

– Demonstrated record of research productivity and publications

Preferred Qualifications:

– Experience with coalescence/IBD methods

– Programming experience (e.g. C/C++, Python/Perl, R)

– Strong mathematical skills

– Experience with genomic data analysis

Salary:

This is a full-time position. Salary is commensurate with qualifications and experience.

How to apply:

Applicants should submit the following materials:

  • A cover letter
  • A curriculum vitae
  • One-page statement of research interests and future goals
  • List of relevant publications
  • Contact information for 3 referees

Send the above combined into a single PDF to Gregory Lanzaro (gclanzaro@ucdavis.edu).

Review of applications will start immediately. This position will be open until filled. The anticipated start date for this position is late 2018 or early 2019. The appointment is for a duration of two years.

The University of California is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age or protected veteran status. For the complete University of California nondiscrimination and affirmative action policy see:

http://policy.ucop.edu/doc/4000376/NondiscrimAffirmAct.

Mark Hanemaaijer has left the VGL to move back to the Netherlands with his fiancé. Congratulations Mark and we wish you all the best on your new adventures!

Parker Houston has been awarded a Provost Undergraduate Fellowship. Congrats Parker!

Greg’s talk on Ecological considerations for gene drive systems is published online from HSTalks. The link is available from the Reports & Press tab of the Publications page. Other talks within the series are presented by some of our collaborators.

Mark Hanemaaijer won second place for best talk at the UC Davis Postdoctoral Research Symposium. Congratulations Mark!

Parker Houston was selected to give an oral presentation at the UC Davis Undergraduate Research Conference. Attendance is free and open to the public. Parker will be speaking on Saturday, April 28th.

Anopheles coluzzii paper published in Parasites & Vectors.

Mark Hanemaaijer and Parker Houston’s paper was published in F1000 Research. Congrats Mark and Parker!

2017

DARPA Safe Genes project begins: The Vector Genetics Lab is part of a large collaboration with several other UC teams on a project to study gene drive in local mosquito populations.

UCIMI project is established: The Vector Genetics Lab will be a part of a project aimed at testing genetically modified mosquitoes in field sites around Africa.

2016

Brad’s paper on An. arabiensis host preference is featured on the PLoS Genetics First page on the week of Sep 15, 2016.

2015

The Verge covers Norris et al. 2015 PNAS paper.

Smithsonian.com Smart News covers Norris et al. 2015 PNAS paper.

Science 2.0 covers Norris et al. 2015 PNAS paper.

The Davis Enterprise covers Norris et al. 2015 PNAS paper.

2014

F1000Research lists Sanford et al. 2014 as Featured Article on the week of Oct. 31. 2014. 

Entomology & Nematology News covers UC Davis Researchers participating in 2014 Bay Area World Malaria Day Symposium.

UC Davis CAES NewsBeat covers our PNAS paper (Lee et al. 2013).

2013

F1000 Prime Article Recommendation recommends our PNAS paper (Lee et al. 2013). [PDF copy]

HEALTHCANAL covers our finding reported on PNAS (Lee et al. 2013). [PDF copy]

BRIC recommends our PNAS paper (Lee et al. 2013) for recognition of outstanding research by a Korean scientist

2011

Wingbeats 2011 summer edition introduces Vector Genetics Laboratory

2010

BioMed Central Open Data Award: Yoosook Lee wins the first Open Data Award with her publication at the Malaria Journal published in 2009 at the BioMed Central’s 4th Annual Research Awards.

2010 Entomological Society of America Professional Awards: Yoosook Lee wins the Journal of Medical Entomology Editor’s Choice Award at the 58th Annual ESA Meeting (Lee et al. 2009. JME).

BioMed Central Press Release: BioMed Central celebrates excellence in open access publishing.

Microsoft Research Connections Blog: Post about the First Open Data Award sponsored by Microsoft.

Science in the Open (Cameron Neylon Blog): The BMC 10th Anniversary Celebrations and Open Data Prize.

EurekAlert Coverage of the 4th BioMed Central Annual Research Awards : BioMed Central celebrates excellence in open-access publishing.

2007

2007 Award for Excellence in Research : Gregory Lanzaro receives Award for Excellence in Research. See the photos of this event here.